Article
Chemistry, Physical
Piero Procacci, Guido Guarnieri
Summary: In this paper, blind predictions for the binding of WP6 with ammonium/diammonium cationic guests in the ninth challenge of SAMPL are presented. The binding free energies were calculated using a virtual double system single box approach and compared with previous submissions. The results show acceptable performance with higher accuracy than previous challenges, indicating the reliability of nonequilibrium approaches for binding free energy calculations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Piero Procacci
Summary: Computational approaches are crucial in modern drug design, but traditional methods face sampling issues. Switching to nonequilibrium alchemical techniques can effectively tackle this problem.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Physical
Joe Z. Wu, Solmaz Azimi, Sheenam Khuttan, Nanjie Deng, Emilio Gallicchio
Summary: The alchemical transfer method (ATM) is presented for calculating standard binding free energies of noncovalent molecular complexes, which is straightforward and applicable with any force field without requiring soft-core pair potentials. The method and its implementation have been validated on the SAMPL6 SAMPLing host-guest benchmark set.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Gerhard Koenig, Benjamin Ries, Philippe H. Huenenberger, Sereina Riniker
Summary: Alchemical free energy calculations often require intermediate states along a coupling parameter lambda to ensure phase space overlap for converged results. The lambda-EDS scheme combines minimum variance pathway and EDS methods to improve sampling efficiency, allowing larger steps along the alchemical pathway and eliminating the need for soft-core potentials.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Markus Fleck, Marcus Wieder, Stefan Boresch
Summary: In calculations of relative free energy differences, the introduction of dummy atoms is necessary to ensure that their contribution does not influence the result. It is important to make sure that dummy atoms only give a multiplicative contribution to the partition function and maintain their position and orientation relative to the physical system. The treatment of dummy atoms can have a significant impact on the computation results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Maria M. Reif, Martin Zacharias
Summary: This study presents an approach combining alchemical modifications and physical-pathway methods to calculate absolute binding free energies. It demonstrates the successful use of simultaneous alchemical transformations and physical ligand unbinding for potential of mean force calculations and nonequilibrium pulling simulations, as well as the benefits of reducing ligand-protein interactions prior to potential of mean force calculations. These methods show promise in reducing sampling problems and improving efficiency in protein-protein binding free energy calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Review
Chemistry, Physical
Michail Papadourakis, Hryhory Sinenka, Pierre Matricon, Jerome Henin, Grace Brannigan, Laura Perez-Benito, Vineet Pande, Herman van Vlijmen, Chris de Graaf, Francesca Deflorian, Gary Tresadern, Marco Cecchini, Zoe Cournia
Summary: This article reviews the progress in alchemical free energy calculations of membrane proteins, focusing on best practices and critical aspects of simulations on G-protein-coupled receptors, ion channels, transporters, and protein-lipid interactions. The study reveals the valuable application of alchemical free energy calculations in drug discovery for membrane-associated proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter Coveney
Summary: The binding free energy between a ligand and its target protein is crucial in the drug discovery process. This study examines the reproducibility of computing alchemical relative binding free energies across different molecular dynamics packages and free energy estimators. The results show good agreement between packages, indicating their consistency in calculating binding free energies.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Dharmeshkumar Patel, Jagdish Suresh Patel, F. Marty Ytreberg
Summary: Protein-protein binding is crucial for biological processes, and accurately estimating the change in binding free energy is important for answering biological questions. While nonrigorous free-energy methods are faster, rigorous alchemical molecular dynamics-based methods are more accurate.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Qing Wen, Hao Fu, Zhen-yu Wang, Ying-de Huang, Zhen-jiang He, Cheng Yan, Jing Mao, Kehua Dai, Xia-hui Zhang, Jun-chao Zheng
Summary: This study proposes a strategy of interfacial engineering and in situ etching to address the challenges of zinc dendrites and side reactions in aqueous rechargeable zinc ion batteries. By introducing a zinc l-cysteine functional layer, the hydrophobicity of the zinc anode is improved, corrosion is mitigated, and uniform zinc deposition is guided. In addition, in situ etching of the zinc foil increases the electrochemical surface area and reduces interfacial resistance. The experimental results show that the Cys-Zn-coated zinc anode exhibits excellent cycling and rate performance.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
Article
Chemistry, Physical
Shunzhou Wan, Agastya P. Bhati, Peter V. Coveney
Summary: Alchemical relative binding free energy calculations have important applications in drug optimization. A comparative study of equilibrium and nonequilibrium methods across a large data set shows that the nonequilibrium method can achieve comparable accuracy and precision to the equilibrium method if ensemble methods are applied. However, the nonequilibrium method introduces higher computational complexity, longer computational time, and may require rerunning the entire set of transitions, increasing computational costs.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat K. Pal, Emilio Gallicchio
Summary: We propose an extension of the alchemical transfer method (ATM) called ATM-RBFE for estimating relative binding free energies of molecular complexes. The method is implemented in the OpenMM molecular simulation package and aims to provide a simpler and more generally applicable route to the calculation of relative binding free energies. The method is validated against benchmark sets and yields consistent and converged estimates in agreement with reference values and experimental measurements.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Finlay Clark, Graeme Robb, Daniel J. Cole, Julien Michel
Summary: Alchemical absolute binding free energy calculations are increasingly important in drug discovery. Multiple distance restraints between anchor points in the receptor and ligand provide a framework without inherent instabilities and can improve convergence. However, calculating the free energy of releasing these restraints is challenging. This study proposes a method to rigorously calculate the free energies of binding with multiple distance restraints by imposing intramolecular restraints on the anchor points.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Organic
Zhe Zhou, Zachary S. Sales, Daniel J. Pippel, Michael Qian, Connor L. Martin
Summary: We present a photocatalyst-free, diastereoselective decarboxylative alkylation method for (hetero)aryl sulfinimines using redox-active esters under blue light. This mild and efficient protocol demonstrates its utility as a versatile synthetic tool, especially for medicinal chemists.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Ning Wang, Ryan S. DeFever, Edward J. Maginn
Summary: Ionic liquids (ILs) have shown potential for applications involving differential gas solubility. However, accurately estimating full solubility isotherms in ILs is important but challenging. In this study, we developed a method using Hamiltonian replica exchange molecular dynamics combined with alchemical free energy calculations to predict full solubility isotherms. Our results matched experimental data well and we successfully predicted solubility trends in IL mixtures that have not been reported before. This method has the potential to be used for solubility prediction and computational screening of ILs for gas separation applications.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Piero Procacci, Guido Guarnieri
Summary: In the context of the SAMPL7 challenge, we computed the standard binding free energy using a non-equilibrium alchemical technique for two series of host-guest systems. The NE alchemy performed well and revealed some important deficiencies of the GAFF2 non-polarizable force field, although overall performances were acceptable and similar to previous challenges.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Hasret Subak, Giulia Selvolini, Marina Macchiagodena, Dilsat Ozkan-Ariksoysal, Marco Pagliai, Piero Procacci, Giovanna Marrazza
Summary: This study presents a voltammetric aptasensor for detecting deoxynivalenol (DON) mycotoxin, with insights gained from a computational study on the molecular mechanisms of interaction. The competitive format approach was successful in achieving a detection limit of 3.2 ng.mL(-1) within a 1-hour detection time, showing promising results for potential applications in food safety.
BIOELECTROCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Piero Procacci
Summary: Computational approaches are crucial in modern drug design, but traditional methods face sampling issues. Switching to nonequilibrium alchemical techniques can effectively tackle this problem.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lorenzo Casbarra, Piero Procacci
Summary: The study demonstrates that Autodock4 performs surprisingly well in absolute binding free energy predictions, outperforming expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable cost-benefit ratio. Interesting features of Autodock4 predictions are revealed, providing valuable insights on the overall reliability of docking screening campaigns in drug discovery projects.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Chemistry, Medicinal
Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Piero Procacci
Summary: The paper presents a protocol for computing absolute dissociation free energy using GROMACS code and PLUMED library, which has been automated with a Python middleware. This protocol enables accurate estimates of dissociation constants in drug-receptor systems at the atomistic level, utilizing advanced sampling techniques and nonequilibrium alchemical methodologies. The protocol has been successfully applied to calculating the absolute dissociation free energy of PF-07321332 with the main protease (3CL(pro)) of SARS-CoV-2, showing potential for precise calculations in similar systems.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Piero Procacci, Marina Macchiagodena
Summary: In the recent SAMPL6 SAMPLing challenge, a simple explanation for the errors observed in the NS-DSSB approach when using unidirectional estimates was proposed, along with a suggestion for a straightforward modification of the protocol to obtain reliable unidirectional estimates for the decoupling and recoupling process of the ligand.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemical Research Methods
Marina Macchiagodena, Marco Pagliai, Piero Procacci
Summary: The study examined the non-covalent interaction between PF-07321332 and the SARS-CoV-2 main protease using computational methods. It found that the binding is likely to be stronger when the catalytic dyad is in a neutral state.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Chemistry, Physical
Piero Procacci, Guido Guarnieri
Summary: In this paper, blind predictions for the binding of WP6 with ammonium/diammonium cationic guests in the ninth challenge of SAMPL are presented. The binding free energies were calculated using a virtual double system single box approach and compared with previous submissions. The results show acceptable performance with higher accuracy than previous challenges, indicating the reliability of nonequilibrium approaches for binding free energy calculations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Piero Procacci
Summary: In the field of drug design, a dual topology alchemical approach for calculating binding free energy between different compounds is proposed. This method overcomes the limitations of traditional single topology methods and has been validated in various test scenarios. It is specifically designed for high-performance computing facilities and can be easily implemented in popular simulation software.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Marina Macchiagodena, Marco Pagliai, Piero Procacci
Summary: We present a step-by-step protocol and toolkit for calculating the relative dissociation free energy (RDFE) using the GROMACS molecular dynamics package. This approach, based on a novel bidirectional nonequilibrium alchemical method, accurately computes RDFE between small molecules with different volume, charge, and chemical topology. The methodology is demonstrated using the challenging SAMPL9 batch of host-guest pairs. The article is supported by an online tutorial and a public Zenodo repository.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Marina Macchiagodena, Gavino Bassu, Irene Vettori, Emiliano Fratini, Piero Procacci, Marco Pagliai
Summary: This study investigates the structural properties of 2-butanol aqueous solutions at different concentrations using both experimental and computational methods. It has been found that 2-butanol tends to form aggregates at concentrations above 1 M, which affects the structural and dynamic properties of the solvent.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Piero Procacci, Guido Guarnieri
Summary: We describe our blind prediction of the toluene-water partition coefficients in the SAMPL9 challenge. We used an efficient MD-based nonequilibrium alchemical technique relying on the GAFF2 non-polarizable force field. The prediction was optimized based on a pre-assessment comparing with known experimental data and provides valuable insights for improving the performance of the force field in drug-receptor system calculations.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Piero Procacci
Summary: This study tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for sampling in two macrocyclic hosts and a drug-receptor system. The results showed that enhanced sampling techniques were necessary for reliable sampling in the macrocycle with long-lived metastable states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Piero Procacci, Marina Macchiagodena, Marco Pagliai, Guido Guarnieri, Francesco Iannone
CHEMICAL COMMUNICATIONS
(2020)
Review
Cell Biology
Gabriella Caminati, Piero Procacci
NEURAL REGENERATION RESEARCH
(2020)
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)